Jeffrey L Thorne

Summary

Affiliation: North Carolina State University
Country: USA

Publications

  1. ncbi request reprint Divergence time and evolutionary rate estimation with multilocus data
    Jeffrey L Thorne
    Bioinformatics Research Center, Box 7566, North Carolina State University, Raleigh, North Carolina 27695 7566, USA
    Syst Biol 51:689-702. 2002
  2. ncbi request reprint Quantifying the impact of protein tertiary structure on molecular evolution
    Sang Chul Choi
    Bioinformatics Research Center, North Carolina State University, NC, USA
    Mol Biol Evol 24:1769-82. 2007
  3. doi request reprint Rates of nucleotide substitution in Cornaceae (Cornales)-Pattern of variation and underlying causal factors
    Qiu Yun Jenny Xiang
    Department of Plant Biology, North Carolina State University, Gardner Hall 2115, Campus Box 7612, Raleigh, NC 27695, USA
    Mol Phylogenet Evol 49:327-42. 2008
  4. pmc Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences
    Sang Chul Choi
    Bioinformatics Research Center, North Carolina State University, Box 7566, Raleigh, NC 27695 7566, USA
    Philos Trans R Soc Lond B Biol Sci 363:3931-9. 2008
  5. pmc Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data
    Tae Kun Seo
    Bioinformatics Research Center, North Carolina State University, Box 7566, Raleigh, NC 27695 7566, USA
    Proc Natl Acad Sci U S A 102:4436-41. 2005
  6. pmc Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci
    Sang Chul Choi
    Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695 7566, USA
    Gene 441:45-52. 2009
  7. ncbi request reprint Time flies, a new molecular time-scale for brachyceran fly evolution without a clock
    Brian M Wiegmann
    Department of Entomology, North Carolina State University, Raleigh, North Carolina 27695, USA
    Syst Biol 52:745-56. 2003
  8. ncbi request reprint Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences
    Tae Kun Seo
    Bioinformatics Research Center, Box 7566, North Carolina State University, NC, USA
    Mol Biol Evol 21:1201-13. 2004
  9. ncbi request reprint Dependence among sites in RNA evolution
    Jiaye Yu
    Bioinformatics Research Center, North Carolina State University, USA
    Mol Biol Evol 23:1525-37. 2006
  10. ncbi request reprint Protein evolution with dependence among codons due to tertiary structure
    Douglas M Robinson
    Bioinformatics Research Center, North Carolina State University, USA
    Mol Biol Evol 20:1692-704. 2003

Detail Information

Publications18

  1. ncbi request reprint Divergence time and evolutionary rate estimation with multilocus data
    Jeffrey L Thorne
    Bioinformatics Research Center, Box 7566, North Carolina State University, Raleigh, North Carolina 27695 7566, USA
    Syst Biol 51:689-702. 2002
    ..The fact that evolutionary rates and times are confounded when sequence data are compared is emphasized and the importance of fossil information for disentangling rates and times is stressed...
  2. ncbi request reprint Quantifying the impact of protein tertiary structure on molecular evolution
    Sang Chul Choi
    Bioinformatics Research Center, North Carolina State University, NC, USA
    Mol Biol Evol 24:1769-82. 2007
    ..Although their influences on rates of evolution vary among protein families, we find that the mean impacts of solvent accessibility and pairwise interactions are about the same...
  3. doi request reprint Rates of nucleotide substitution in Cornaceae (Cornales)-Pattern of variation and underlying causal factors
    Qiu Yun Jenny Xiang
    Department of Plant Biology, North Carolina State University, Gardner Hall 2115, Campus Box 7612, Raleigh, NC 27695, USA
    Mol Phylogenet Evol 49:327-42. 2008
    ..This was particularly pronounced in the dwarf dogwood lineage, in which genome-wide acceleration in both molecular and morphological evolution has likely occurred...
  4. pmc Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences
    Sang Chul Choi
    Bioinformatics Research Center, North Carolina State University, Box 7566, Raleigh, NC 27695 7566, USA
    Philos Trans R Soc Lond B Biol Sci 363:3931-9. 2008
    ..We then show how to modify the neutral model so that its stationary distribution at the amino acid level can match a profile hidden Markov model, such as the one associated with the Pfam database...
  5. pmc Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data
    Tae Kun Seo
    Bioinformatics Research Center, North Carolina State University, Box 7566, Raleigh, NC 27695 7566, USA
    Proc Natl Acad Sci U S A 102:4436-41. 2005
    ..We discuss the applicability of the two-stage bootstrap idea to the Kishino-Hasegawa test and the Shimodaira-Hasegawa test...
  6. pmc Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci
    Sang Chul Choi
    Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695 7566, USA
    Gene 441:45-52. 2009
    ..We find that our technique for employing protein tertiary structure information yields some biologically plausible results but that it does not substantially improve the inference of ancestral human allele types...
  7. ncbi request reprint Time flies, a new molecular time-scale for brachyceran fly evolution without a clock
    Brian M Wiegmann
    Department of Entomology, North Carolina State University, Raleigh, North Carolina 27695, USA
    Syst Biol 52:745-56. 2003
    ..This study provides increased resolution of brachyceran phylogeny, and our revised estimates of fly ages should improve the temporal context of evolutionary inferences and genomic comparisons between fly model organisms...
  8. ncbi request reprint Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences
    Tae Kun Seo
    Bioinformatics Research Center, Box 7566, North Carolina State University, NC, USA
    Mol Biol Evol 21:1201-13. 2004
    ..Our analysis of these data also suggests that rates have been positively correlated...
  9. ncbi request reprint Dependence among sites in RNA evolution
    Jiaye Yu
    Bioinformatics Research Center, North Carolina State University, USA
    Mol Biol Evol 23:1525-37. 2006
    ..Potential applications of this procedure, including improved ancestral sequence inference and location of functionally interesting sites, are discussed...
  10. ncbi request reprint Protein evolution with dependence among codons due to tertiary structure
    Douglas M Robinson
    Bioinformatics Research Center, North Carolina State University, USA
    Mol Biol Evol 20:1692-704. 2003
    ....
  11. ncbi request reprint Testing for spatial clustering of amino acid replacements within protein tertiary structure
    Jiaye Yu
    Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695 7566, USA
    J Mol Evol 62:682-92. 2006
    ..These findings need to be reconciled with the common practice of basing evolutionary inferences on models that assume independent change among sites...
  12. pmc History can matter: non-Markovian behavior of ancestral lineages
    Reed A Cartwright
    Department of Genetics, Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695 7566, USA
    Syst Biol 60:276-90. 2011
    ..As a result, we believe that increased attention needs to be devoted to the robustness of evolutionary inference procedures that rely upon the Markov assumption...
  13. pmc Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach
    Elizabeth H Scholl
    Center for the Biology of Nematode Parasitism, Box 7253, North Carolina State University, Raleigh, NC 27695, USA
    Genome Biol 4:R39. 2003
    ..We present a method for a high-throughput genome screen for horizontally acquired genes, illustrated using expressed sequence tag (EST) data from three species of root-knot nematode, Meloidogyne species...
  14. ncbi request reprint Population genetics without intraspecific data
    Jeffrey L Thorne
    Wissenschaftskolleg zu Berlin, Institute for Advanced Study, Berlin, Germany
    Mol Biol Evol 24:1667-77. 2007
    ..We argue that statistical fit to data should not be the sole criterion for assessing models of sequence change. A good interspecific model should also yield a clear and biologically plausible population genetic interpretation...
  15. ncbi request reprint Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution
    Masami Hasegawa
    The Institute of Statistical Mathematics, Minato ku, Tokyo, Japan
    Genes Genet Syst 78:267-83. 2003
    ..With denser taxonomic sampling and a more realistic model of molecular evolution, this Bayesian approach is expected to increase the accuracy of divergence time estimates...
  16. ncbi request reprint Protein evolution constraints and model-based techniques to study them
    Jeffrey L Thorne
    Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193 Berlin, Germany
    Curr Opin Struct Biol 17:337-41. 2007
    ....
  17. pmc Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach
    Tae Kun Seo
    Department of Biosystems Science, The Graduate University for Advanced Studies, Hayama, Kanagawa, 240 0193, Japan
    Genetics 160:1283-93. 2002
    ..52 x 10(-5) to 5.02 x 10(-5). Our results indicate that effective viral population size and evolutionary rate per year are negatively correlated among HIV-1 patients...
  18. ncbi request reprint A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times
    Tae Kun Seo
    Department of Biosystems Science, The Graduate University for Advanced Studies, Hayama, Kanagawa, 240 0193, Japan
    Bioinformatics 18:115-23. 2002
    ..Variation in isolation times can be intentionally adjusted to increase the power of hypothesis tests and to reduce the uncertainty of evolutionary parameter estimates, but this fact has received little previous attention...